I would try it again at the check-in desk at JFK. Maybe ask them for the status of your upgrade, act surprised when they tell you it was denied. Ask if there are any seats unsold, if yes, can you have one, etc.

If you strike out at JFK, I would head straight to the RCC once you land at NRT and go through it again. In the event NRT can upgrade you, they may insist on taking another SWU. It'll be your choice whether you want to fight with MP afterwards on why you should have only paid with one.

Sometimes persistence can pay off. Otherwise, hope the op-upgrade fairy pays you a visit.